{"doi":"10.1186/s13059-024-03317-4","title":"Detection of allele-specific expression in spatial transcriptomics with spASE","abstract":"Spatial transcriptomics technologies permit the study of the spatial distribution of RNA at near-single-cell resolution genome-wide. However, the feasibility of studying spatial allele-specific expression (ASE) from these data remains uncharacterized. Here, we introduce spASE, a computational framework for detecting and estimating spatial ASE. To tackle the challenges presented by cell type mixtures and a low signal to noise ratio, we implement a hierarchical model involving additive mixtures of spatial smoothing splines. We apply our method to allele-resolved Visium and Slide-seq from the mouse cerebellum and hippocampus and report new insight into the landscape of spatial and cell type-specific ASE therein.","journal":"Genome biology","year":2024,"id":435506,"datarank":0.5223229555940634,"base_score":2.5649493574615367,"endowment":2.5649493574615367,"self_citation_contribution":0.38474240361923057,"citation_network_contribution":0.13758055197483285,"self_endowment_contribution":0.38474240361923057,"citer_contribution":0.13758055197483285,"corpus_percentile":null,"corpus_rank":null,"citation_count":12,"citer_count":12,"citers_with_citation_signal":9,"citers_with_endowment":9,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9589,"is_data_producer":true,"deposit_databanks":{"GEO":["GSE268519, GSE118987"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":614450,"name":"Dylan Cable","orcid":"0000-0001-7042-2960","position":1,"is_corresponding":false},{"id":55250,"name":"Irving Barrera","orcid":"0000-0001-6099-4316","position":2,"is_corresponding":false},{"id":87726,"name":"Tongtong Zhao","orcid":"0000-0001-8079-8048","position":3,"is_corresponding":false},{"id":35220,"name":"Evan Murray","orcid":"0000-0002-9195-7478","position":4,"is_corresponding":false},{"id":42117,"name":"Martin J. Aryee","orcid":"0000-0002-6848-1344","position":5,"is_corresponding":false},{"id":24055,"name":"Fei Chen","orcid":"0000-0003-2308-3649","position":6,"is_corresponding":false},{"id":31703,"name":"Rafael A. Irizarry","orcid":"0000-0002-3944-4309","position":7,"is_corresponding":false},{"id":616475,"name":"Luli S. Zou","orcid":null,"position":0,"is_corresponding":true}],"reference_count":73,"raw_metadata":null,"created_at":"2026-07-19T02:00:08.103086Z","pmid":"38978101","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}